PDB file 1TTT

This file depicts the elongation factor EF-Tu with bound GDPNP, a non-hydrolyzable GTP analog, and Phe-tRNAPhe. The structure was solved by P. Nissen, M. Kjeldgaard, S. Thirup, G. Polekhina, L. Reshetnikova, B. Clark, & J. Nyborg  in 1995.

Suggested display options:

To simplify the display of this crystal whose unit structure includes 3 copies of the protein, select all, and then select hide selected.

Select chain a (or use command line to select *a), to view one copy of EF-Tu, display as cartoons, and color chain.
chain d (or use command line to select *d) to view the tRNA bound to EF-Tu, display as wireframe, and color CPK.
To identify the end of the acceptor stem, type in "
select 76d, 77d" and display as sticks.
Identify the the terminal adenosine and the bound phenylalanine.
might be the significance of the observation that the acceptor stem is embedded in the protein?

To visualize the GTP analog select gnpa, display as spacefill, and color CPK.
Identify the nitrogen that substitutes for phosphorous in the GTP analog GDPNP.
Separately select
mg*a, display as spacefill, and color CPK. Note the position of the magnesium.

To have a frame of reference in comparing to the structure with bound GDP, give the following residues the colors indicated, but do not change their display from cartoons:

Rotate so that the C-terminus (in yellow) is centered at the bottom and pointing leftward, and the ligand (GDPNP) is in front.
Compare to the structure of the same protein complexed with GDPNP but lacking tRNA.
Question: Which makes the larger difference in structure, tRNA or GDP vs GDPNP (GTP)?

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